On 4 December 1990, Ardzinba was elected Chairman of the Supreme Soviet of Abkhazia.[1] Ardzinba, a charismatic but excitable figure popular among the Abkhaz was believed by Georgians to have helped to instigate the violence of July 1989.[3] Ardzinba managed to consolidate his power relatively quickly and reneged on pre-election promises to increase the representation of Georgians in Abkhazia's autonomous structures; since then, Ardzinba tried to rule Abkhazia relatively single-handedly, but avoided, for the time being, overt conflict with the central authorities in Tbilisi. In mid-1991, he negotiated and accepted the Georgian concession on the reform of the electoral law that granted the Abkhaz wide over-representation in the Supreme Soviet. However, Ardzinba created the Abkhazian National Guard that was mono-ethnically Abkhaz, and initiated a practice of replacing ethnic Georgians in leading positions with Abkhaz. As the Georgian-Abkhaz tensions rose, Ardzinba's rhetoric mounted, as he claimed in late July 1992 that "Abkhazia is strong enough to fight Georgia."[4]

In August 1992, a Georgian military force ousted Ardzinba and his group from Sukhumi. They took shelter in Gudauta, a home to the Soviet-era Russian military base. Ardzinba benefited from his contacts with the Russian hardliner circles and military leaders to garner critical support in the war against the Georgian government.[5]

After the hostilities ended in 1994 and the bulk of the Georgian population was forced out of Abkhazia, the Abkhazian parliament elected Ardzinba to the presidency, a move that was condemned by Georgia and the United Nations as illegal[citation needed]. He won the first direct polls on 3 October 1999, without an opponent and was re-elected as president of Abkhazia.[6] He installed an autocratic regime[7] and remained politically untouchable until his health seriously deteriorated in 2003. He once stated that independence from Georgia is not negotiable, and he has tried to align the state with Russia, whose political and economic support was essential to the republic. As a leader of the Abkhaz side he met the two successive Russian presidents, Boris Yeltsin and Vladimir Putin, as well as a President of Georgia, Eduard Shevardnadze.

Under his rule, human rights records were extremely poor as most of the pre-war Georgian population of Abkhazia were deprived the right to return, and those who remained were subjected to systematic ethnic cleansing[citation needed]. Ardzinba aroused some further criticism from the international community after issuing a decree banning Jehovah's Witnesses in 1995[citation needed].

During the last years of his presidency Ardzinba faced criticism for both failing to bring stability to Abkhazia and his increasingly low public profile. He had not appeared in public since 2002. As a result, the role of governing the state had been increasingly left to Prime Minister Raul Khajimba.

He had been in extremely poor health and underwent treatment in Moscow for some time. Despite increasing calls from the opposition (particularly the Amtsakhara movement) for him to resign he had stated that he would finish his term, which was supposed to end in October 2004, but in fact did not end until 12 February 2005, due to disputes over the election of his successor. There were also calls for him to be impeached. However, although the Abkhaz Constitution allows for impeachment, the process would likely have not been completed before the end of his term, so no serious steps were taken to bring it about. He was unable to run for a third term due to constitutional restrictions, and it is unlikely that his health would have enabled him to do so even if this was allowed.

He was replaced by the winner of the presidential election of 12 January 2005, Sergei Bagapsh. A previous election had been held in late 2004 after the murder of opposition leader Garri Aiba, but the result was controversial.

By 2010, Ardzinba's health was in decline and had been for some time.[8][9] Ardzinba died on 4 March 2010, at the age of 64.[1] He was in the Central Clinical Hospital in Moscow at the time.[1] He had been escorted there the previous week.[9] The cause of death was not been released to the public.[1][10] He is survived by his wife and daughter.[1] The President of Abkhazia, Sergei Bagapsh, paid tribute: "His service to the Abkhaz people was boundless".[1] Three days of mourning were declared in Abkhazia in remembrance of Ardzinba.[11]